Publications / further reading

Recent papers from NMR Centre researchers

2023

"UnidecNMR: Automatic peak detection for NMR spectra in 1-4 dimensions." (2023) Buchanan C, Karunanithy G, Tkachenko O, Barber M, Marty M, Redfield C, Nott T, Baldwin A.J. Nature Communications, in press. https://europepmc.org/article/ppr/ppr575578

"Posttranslational, site-directed photochemical fluorine editing of protein sidechains to probe residue oxidation state via (19)F-nuclear magnetic resonance." (2023) Isenegger, P. G., Josephson, B., Gaunt, B., Davy, M. J., Gouverneur, V., Baldwin, A. J., & Davis, B. G. Nat Protoc, 18(5), 1543. https://doi.org/10.1038/s41596-022-00800-9

"Efficiently computing the Uhlmann fidelity for density matrices." (2023) Baldwin A.J., Jones J.A. Phys Rev A, 107, 012427. https://journals.aps.org/pra/abstract/10.1103/PhysRevA.107.012427

2022

"Quantitative High-Field NMR- and Mass Spectrometry-Based Fatty Acid Sequencing Reveals Internal Structure in Ru-Catalyzed Deuteration of Docosahexaenoic Acid." (2022) Wang, DH, Vidovic, D, McKay, AI, Darwish, T, Park, HG, Garza, SM et al. & Shchepinov, MS. Anal Chem, 94(38), 12971. https://doi.org/10.1021/acs.analchem.2c00923

"Pathogen-sugar interactions revealed by universal saturation transfer analysis." (2022) Buchanan, CJ, Gaunt, B, Harrison, PJ, Yang, Y, Liu, J, Khan, A et al. & Davis, BG Science, 377(6604), eabm3125. https://doi.org/10.1126/science.abm3125

"Reductive site-selective atypical C,Z-type/N2-C2 cleavage allows C-terminal protein amidation." (2022) Mollner TA, Giltrap AM, Zeng Y, Demyanenko Y, Buchanan C, Oehlrich D, Baldwin AJ, Anthony, DC, Mohammed S, Davis BG.  Science Advances , 8(14). https://doi.org/10.1126/sciadv.abl8675

2021

"The 'Shape-Shifter' Peptide from the Disulphide Isomerase PmScsC Shows Context-Dependent Conformational Preferences." (2021) Smith, L. J., Green, C. W., & Redfield, C. Biomolecules, 11(5). https://doi.org/10.3390/biom11050642

"Post-translational insertion of boron in proteins to probe and modulate function." (2021) Mollner, T. A., Isenegger, P. G., Josephson, B., Buchanan, C., Lercher, L., Oehlrich, D. et al. & Davis, B. G. Nat Chem Biol, 17(12), 1245. https://doi.org/10.1038/s41589-021-00883-7

"Conformational triggers associated with influenza matrix protein 1 polymerization." (2021) Mohd-Kipli, F., Claridge, J. K., Habjanič, J., Jiang, A., & Schnell, J. R. J Biol Chem, 296, 100316. https://doi.org/10.1016/j.jbc.2021.100316

"Structural characterization of KKT4, an unconventional microtubule-binding kinetochore protein." (2021) Ludzia, P., Lowe, E. D., Marcianò, G., Mohammed, S., Redfield, C., & Akiyoshi, B. Structure, 29(9), 1014. https://doi.org/10.1016/j.str.2021.04.004

"The structural basis for high affinity binding of α1-acid glycoprotein to the potent antitumor compound UCN-01." (2021) Landin, E. J. B., Williams, C., Ryan, S. A., Bochel, A., Akter, N., Redfield, C. et al. & Crump, M. P. J Biol Chem, 297(6), 101392. https://doi.org/10.1016/j.jbc.2021.101392

"Toxin import through the antibiotic efflux channel TolC." (2021) Housden, N. G., Webby, M. N., Lowe, E. D., El-Baba, T. J., Kaminska, R., Redfield, C. et al. & Kleanthous, C. Nat Commun, 12(1), 4625. https://doi.org/10.1038/s41467-021-24930-y

2020

"An NMR and MD study of complexes of bacteriophage lambda lysozyme with tetra- and hexa-N-acetylchitohexaose." (2020) Turupcu, A., Bowen, A. M., Di Paolo, A., Matagne, A., Oostenbrink, C., Redfield, C., & Smith, L. J. Proteins, 88(1), 82. https://doi.org/10.1002/prot.25770

"Light-driven post-translational installation of reactive protein side chains." (2020) Josephson, B., Fehl, C., Isenegger, P. G., Nadal, S., Wright, T. H., Poh, A. W. J. et al. & Davis, B. G. Nature, 585(7826), 530. https://doi.org/10.1038/s41586-020-2733-7

"The lipoprotein Pal stabilises the bacterial outer membrane during constriction by a mobilisation-and-capture mechanism." (2020) Szczepaniak, J., Holmes, P., Rajasekar, K., Kaminska, R., Samsudin, F., Inns, P. G. et al. & Kleanthous, C. Nat Commun, 11(1), 1305. https://doi.org/10.1038/s41467-020-15083-5

"Local frustration determines loop opening during the catalytic cycle of an oxidoreductase." (2020) Stelzl, L. S., Mavridou, D. A., Saridakis, E., Gonzalez, D., Baldwin, A. J., Ferguson, S. J. et al. & Redfield, C. Elife, 9. https://doi.org/10.7554/eLife.54661

"Conformational flexibility of GRASPs and their constituent PDZ subdomains reveals structural basis of their promiscuous interactome." (2020) Mendes, L. F. S., Batista, M. R. B., Judge, P. J., Watts, A., Redfield, C., & Costa-Filho, A. J. Febs j, 287(15), 3255. https://doi.org/10.1111/febs.15206

"(1)H, (13)C and (15)N resonance assignments for the microtubule-binding domain of the kinetoplastid kinetochore protein KKT4 from Trypanosoma brucei." (2020) Ludzia, P., Akiyoshi, B., & Redfield, C. Biomol NMR Assign, 14(2), 309. https://doi.org/10.1007/s12104-020-09968-1

"pH-dependent secondary structure propensity of the influenza A virus M2 cytoplasmic tail." (2020) Claridge, J. K., Mohd-Kipli, F., Florea, A., Gate, T., & Schnell, J. R. Biomol NMR Assign, 14(1), 157. https://doi.org/10.1007/s12104-020-09937-8

2019

"Local unfolding of the HSP27 monomer regulates chaperone activity." (2019) Alderson, T. R., Roche, J., Gastall, H. Y., Dias, D. M., Pritišanac, I., Ying, J. et al. & Baldwin, A. J. Nat Commun, 10(1), 1068. https://doi.org/10.1038/s41467-019-08557-8

"HspB1 phosphorylation regulates its intramolecular dynamics and mechanosensitive molecular chaperone interaction with filamin C." (2019) Collier, M. P., Alderson, T. R., de Villiers, C. P., Nicholls, D., Gastall, H. Y., Allison, T. M. et al. & Benesch, J. L. P. Sci Adv, 5(5), eaav8421. https://doi.org/10.1126/sciadv.aav8421

"Hepatitis C virus sequence divergence preserves p7 viroporin structural and dynamic features." (2019) Oestringer, B. P., Bolivar, J. H., Claridge, J. K., Almanea, L., Chipot, C., Dehez, F. et al. & Zitzmann, N. Sci Rep, 9(1), 8383. https://doi.org/10.1038/s41598-019-44413-x

"Allosteric activation of an ion channel triggered by modification of mechanosensitive nano-pockets." (2019) Kapsalis, C., Wang, B., El Mkami, H., Pitt, S. J., Schnell, J. R., Smith, T. K. et al. & Pliotas, C. Nat Commun, 10(1), 4619. https://doi.org/10.1038/s41467-019-12591-x

"(1)H, (13)C and (15)N resonance assignments for the tandem CUE domains from chromatin remodeler SMARCAD1." (2019) Biasutto, A. J., West, P. M., Mancini, E. J., & Redfield, C. Biomol NMR Assign, 13(2), 261. https://doi.org/10.1007/s12104-019-09888-9

2018

"The CcmC-CcmE interaction during cytochrome c maturation by System I is driven by protein-protein and not protein-heme contacts." (2018) Shevket, S. H., Gonzalez, D., Cartwright, J. L., Kleanthous, C., Ferguson, S. J., Redfield, C., & Mavridou, D. A. I. J Biol Chem, 293(43), 16778. https://doi.org/10.1074/jbc.RA118.005024

"Re-evaluating the p7 viroporin structure." (2018) Oestringer, B. P., Bolivar, J. H., Hensen, M., Claridge, J. K., Chipot, C., Dehez, F. et al. & Schnell, J. R. Nature, 562(7727), E8. https://doi.org/10.1038/s41586-018-0561-9

"Formation of a Secretion-Competent Protein Complex by a Dynamic Wrap-around Binding Mechanism." (2018) Gupta, A. A., Reinartz, I., Karunanithy, G., Spilotros, A., Jonna, V. R., Hofer, A. et al. & Wolf-Watz, M. J Mol Biol, 430(18 Pt B), 3157. https://doi.org/10.1016/j.jmb.2018.07.014

2017

"Exploitation of an iron transporter for bacterial protein antibiotic import." (2017) White, P., Joshi, A., Rassam, P., Housden, N. G., Kaminska, R., Goult, J. D. et al. & Kleanthous, C. Proc Natl Acad Sci U S A, 114(45), 12051. https://doi.org/10.1073/pnas.1713741114

"The N-Terminal Region of Fibrillin-1 Mediates a Bipartite Interaction with LTBP1." (2017) Robertson, I. B., Dias, H. F., Osuch, I. H., Lowe, E. D., Jensen, S. A., Redfield, C., & Handford, P. A. Structure, 25(8), 1208. https://doi.org/10.1016/j.str.2017.06.003

"Proline isomerization in the C-terminal region of HSP27." (2017) Alderson, T. R., Benesch, J. L. P., & Baldwin, A. J. Cell Stress Chaperones, 22(4), 639. https://doi.org/10.1007/s12192-017-0791-z

"Monitoring the Disassembly of Virus-like Particles by (19)F-NMR." (2017) Leung, R. L. C., Robinson, M. D. M., Ajabali, A. A. A., Karunanithy, G., Lyons, B., Raj, R. et al. & Davis, B. G. J Am Chem Soc, 139(15), 5277. https://doi.org/10.1021/jacs.6b11040

"Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory." (2017) Pritišanac, I., Degiacomi, M. T., Alderson, T. R., Carneiro, M. G., Ab, E., Siegal, G., & Baldwin, A. J. J Am Chem Soc, 139(28), 9523. https://doi.org/10.1021/jacs.6b11358

2016

"Non-Linear and Flexible Regions of the Human Notch1 Extracellular Domain Revealed by High-Resolution Structural Studies." (2016) Weisshuhn, P. C., Sheppard, D., Taylor, P., Whiteman, P., Lea, S. M., Handford, P. A., & Redfield, C. Structure, 24(4), 555. https://doi.org/10.1016/j.str.2016.02.010

"Posttranslational mutagenesis: A chemical strategy for exploring protein side-chain diversity." (2016) Wright, T. H., Bower, B. J., Chalker, J. M., Bernardes, G. J., Wiewiora, R., Ng, W. L. et al. & Davis, B. G. Science, 354(6312). https://doi.org/10.1126/science.aag1465

"Harnessing NMR relaxation interference effects to characterise supramolecular assemblies." (2016) Karunanithy, G., Cnossen, A., Müller, H., Peeks, M. D., Rees, N. H., Claridge, T. D. et al. & Baldwin, A. J. Chem Commun (Camb), 52(47), 7450. https://doi.org/10.1039/c6cc02544g

"(1)H, (13)C and (15)N resonance assignments for the response regulator CheY3 from Rhodobacter sphaeroides." (2016) Varela, L., Bell, C. H., Armitage, J. P., & Redfield, C. Biomol NMR Assign, 10(2), 373. https://doi.org/10.1007/s12104-016-9703-x

"The Role of Active Site Flexible Loops in Catalysis and of Zinc in Conformational Stability of Bacillus cereus 569/H/9 β-Lactamase." (2016) Montagner, C., Nigen, M., Jacquin, O., Willet, N., Dumoulin, M., Karsisiotis, A. I. et al. & Matagne, A. J Biol Chem, 291(31), 16124. https://doi.org/10.1074/jbc.M116.719005

2015

"(1)H, (13)C and (15)N assignments of EGF domains 4 to 7 of human Notch-1." (2015a) Weisshuhn, P. C., Handford, P. A., & Redfield, C. Biomol NMR Assign, 9(2), 275. https://doi.org/10.1007/s12104-014-9591-x

"(1)H, (13)C and (15)N assignments of EGF domains 8-11 of human Notch-1." (2015b) Weisshuhn, P. C., Handford, P. A., & Redfield, C. Biomol NMR Assign, 9(2), 375. https://doi.org/10.1007/s12104-015-9613-3

"(1)H, (13)C, and (15)N resonance assignments for the tandem PHD finger motifs of human CHD4." (2015) Walport, L. J., Morra, R., Mancini, E. J., & Redfield, C. Biomol NMR Assign, 9(2), 239. https://doi.org/10.1007/s12104-014-9582-y

"Comparison of the backbone dynamics of wild-type Hydrogenobacter thermophilus cytochrome c(552) and its b-type variant." (2015) Tozawa, K., Ferguson, S. J., Redfield, C., & Smith, L. J. J Biomol NMR, 62(2), 221. https://doi.org/10.1007/s10858-015-9938-3

"Consequences of inducing intrinsic disorder in a high-affinity protein-protein interaction." (2015) Papadakos, G., Sharma, A., Lancaster, L. E., Bowen, R., Kaminska, R., Leech, A. P. et al. & Kleanthous, C. J Am Chem Soc, 137(16), 5252. https://doi.org/10.1021/ja512607r

"Position and orientational preferences of drug-like compounds in lipid membranes: a computational and NMR approach." (2015) Ma, J., Domicevica, L., Schnell, J. R., & Biggin, P. C. Phys Chem Chem Phys, 17(30), 19766. https://doi.org/10.1039/c5cp03218k

"Structure of the terminal PCP domain of the non-ribosomal peptide synthetase in teicoplanin biosynthesis." (2015) Haslinger, K., Redfield, C., & Cryle, M. J. Proteins, 83(4), 711. https://doi.org/10.1002/prot.24758

"A conserved amphipathic helix is required for membrane tubule formation by Yop1p." (2015) Brady, J. P., Claridge, J. K., Smith, P. G., & Schnell, J. R. Proc Natl Acad Sci U S A, 112(7), E639. https://doi.org/10.1073/pnas.1415882112

2014

"An exact solution for R2,eff in CPMG experiments in the case of two site chemical exchange" (2014) Baldwin, AJ. J Magn Reson 244(100):114-24. https://doi.org/10.1016/j.jmr.2014.02.023

"Bacterial expression and in vitro refolding of limited fragments of the Notch receptor and its ligands." (2014) Whiteman, P., Redfield, C., & Handford, P. A. Methods Mol Biol, 1187, 193. https://doi.org/10.1007/978-1-4939-1139-4_15

"NMR spectroscopic and bioinformatic analyses of the LTBP1 C-terminus reveal a highly dynamic domain organisation." (2014) Robertson, I. B., Handford, P. A., & Redfield, C. PLoS One, 9(1), e87125. https://doi.org/10.1371/journal.pone.0087125

"An extended active-site motif controls the reactivity of the thioredoxin fold." (2014) Mavridou, D. A., Saridakis, E., Kritsiligkou, P., Mozley, E. C., Ferguson, S. J., & Redfield, C. J Biol Chem, 289(12), 8681. https://doi.org/10.1074/jbc.M113.513457

"Fragments of bacterial endoglycosidase s and immunoglobulin g reveal subdomains of each that contribute to deglycosylation." (2014) Dixon, E. V., Claridge, J. K., Harvey, D. J., Baruah, K., Yu, X., Vesiljevic, S. et al. & Crispin, M. J Biol Chem, 289(20), 13876. https://doi.org/10.1074/jbc.M113.532812

Example high-impact papers and reviews from the literature showing NMR applications 

2022:

  • Kleist & Volkman et al. (2022) Science "Conformational selection guides β-arrestin recruitment at a biased G protein-coupled receptor" https://doi.org/10.1126/science.abj4922. {Note: methyl-based spectra of biased signalling in a GPCR}
  • Buchanan & Davis et al. (2022) Science "Pathogen-sugar interactions revealed by universal saturation transfer analysis" https://doi.org/10.1126/science.abm3125. {Note: a universal screen for protein-small molecule interactions; data recorded on our 950 MHz spectrometer}
  • Chan & Christodoulou et al. (2022) Nature Chem "The ribosome stabilizes partially folded intermediates of a nascent multi-domain protein" https://doi.org/10.1038/s41557-022-01004-0. {Note: using 19F NMR to watch protein folding on the ribosome}
  • Overbeck & Sprangers et al. (2022) Nature Chem "Observation of conformational changes that underlie the catalytic cycle of Xrn2" https://doi.org/10.1038/s41589-022-01111-6. {Note: uses methyl-based NMR and 19F NMR for insights into conformational dynamics of a 100kDa eukaryotic exoribonuclease}
  • Borggrafe & Etzkorn et al. (2022) Nature "Time-resolved structural analysis of an RNA-cleaving DNA catalyst" https://doi.org/10.1038/s41586-021-04225-4. {Note: NMR conformational studies of DNA and RNA}
  • Bhardwaj & Baker et al. (2022) Cell "Accurate de novo design of membrane-traversing macrocycles" https://doi.org/10.1016/j.cell.2022.07.019. {Note: validation of peptide design, and insights into flexibility}
  • Battacharya & Korendovych et al. (2022) Nature "NMR-guided directed evolution" https://doi.org/10.1038/s41586-022-05278-9. {Note: using chemical shift perturbations to identify mutation hot-spots likely to affect activity}
  • He & Feigon et al. (2022) Nature "Structure of Tetrahymena telomerase-bound CST with polymerase α-primase" https://doi.org/10.1038/s41586-022-04931-7. {Note: NMR used to determine peptide binding to larger complex; also used to model cryoEM density}
  • Still & Kern et al. (2022) Nature "Structure determination of high-energy states in a dynamic protein ensemble" https://doi.org/10.1038/s41586-022-04468-9. {Note: NMR used to identify excited state conformations of a protein}

2021:

  • Cermakova & Veverka et al. (2021) Science "A ubiquitous disordered protein interaction module orchestrates transcription elongation" https://doi.org/10.1126/science.abe2913. {Note: characterise PPIs in intrinsically disordered regions of proteins}
  • Huang & Prosser et al. (2021) Cell "Delineating the conformational landscape of the adenosine A2A receptor during G protein coupling" https://doi.org/10.1016/j.cell.2021.02.041. {Note: 19F NMR for detecting conformational changes in a GPCR embedded in a lipid nanodisc}
  • Reshetnyak & Kalodimos et al. (2021) Nature "Mechanism for the activation of the anaplastic lymphoma kinase receptor" https://doi.org/10.1038/s41586-021-04140-8. {Note: integrating NMR data with structures from XRC and cryoEM}
  • Anishchenko & Baker et al. (2021) Nature "De novo protein design by deep network hallucination" https://doi.org/10.1038/s41586-021-04184-w. {Note: NMR to validate predicted structural models}
  • Science "Evolution of fold switching in a metamorphic protein" https://doi.org/10.1126/science.abd8700. {Note: identification and characterisation of interconverting structural states in solution}
  • Vorobieva & Baker et al. (2021) Science "De novo design of transmembrane β barrels" https://doi.org/10.1126/science.abc8182. {Note: NMR for rapid validation of structures in solution}
  • Perica & Kortemme et al. (2021) Nature "Systems-level effects of allosteric perturbations to a model molecular switch" https://doi.org/10.1038/s41586-021-03982-6. {Note: NMR to study allostery and conformational switches}

2020:

  • Martin & Mittag et al. (2020) Science "Valence and patterning of aromatic residues determine the phase behavior of prion-like domains" https://doi.org/10.1126/science.aaw8653. {Note: site-specific info on dynamics and interactions of an IDP to identify new mechanisms in phase-separating proteins}
  • Wu & Xu et al. (2020) Cell "Multiple Signaling Roles of CD3ε and Its Application in CAR-T Cell Therapy" https://doi.org/10.1016/j.cell.2020.07.018. {Note: observation of immune receptor interactions and role of PTMs}
  • Stelzl & Redfield et al. (2020) ELife "Local frustration determines loop opening during the catalytic cycle of an oxidoreductase" https://doi.org/10.7554/eLife.54661. {Note: measuring motions on a catalytically relevant timescale of µs-ms}
  • Frei & Nietlispach et al. (2020) Nature Comm. "Conformational plasticity of ligand-bound and ternary GPCR complexes studied by 19F NMR of the β1-adrenergic receptor" https://doi.org/10.1038/s41467-020-14526-3. {Note: measuring ligand- and G-protein-induced activation of a GPCR}
  • Xie & Kalodimos et al. (2020) Science "Conformational states dynamically populated by a kinase determine its function" https://doi.org/10.1126/science.abc2754. {Note: identifying conformational intermediates in kinases and cancer-associated variants}

Earlier:

  • Kim & Forman-Kay et al. (2019) Science "Phospho-dependent phase separation of FMRP and CAPRIN1 recapitulates regulation of translation and deadenylation" https://doi.org/10.1126/science.aax4240. {Note: measuring PPIs in membrane-less organelles}
  • Rosenzweig & Kay et al. (2017) ELife "Promiscuous binding by Hsp70 results in conformational heterogeneity and fuzzy chaperone-substrate ensembles" https://doi.org/10.7554/eLife.28030. {Note: demonstrates ability of NMR to deal with heterogeneity and weak interactions}
  • Mylona & Treisman et al. (2016) Science "Opposing effects of Elk-1 multisite phosphorylation shape its response to ERK activation" https://doi.org/10.1126/science.aad1872. {Note: time-resolved 'in cell' NMR of phosphorylation}
  • Huang & Rubinstein et al. (2016) PNAS "Unfolding the mechanism of the AAA+ unfoldase VAT by a combined cryo-EM, solution NMR study" https://doi.org/10.1073/pnas.1603980113 {Note: combined cryoEM and NMR study of a 500kDa homohexamer using post-translational labelling of cysteines}

 

Reviews highlighting application of NMR to challenging biological questions:

  • Studying molecular machines: Rosenzweig & Kay (2014) Annu Rev Biochem "Bringing dynamic molecular machines into focus by methyl-TROSY NMR" https://doi.org/10.1146/annurev-biochem-060713-035829.

  • Measuring biologically relevant dynamics: Alderson & Kay (2021) Cell "NMR spectroscopy captures the essential role of dynamics in regulating biomolecular function" https://doi.org/10.1016/j.cell.2020.12.034.

  • Overview of recent high impact work using NMR: Sekhar & Kay (2019) Annu Rev Biophys "An NMR View of Protein Dynamics in Health and Disease" https://doi.org/10.1146/annurev-biophys-052118-115647.

  • How the NMR approach benefits from AlphaFold2: Laurents (2022) Front Mol Biosci "AlphaFold 2 and NMR Spectroscopy: Partners to Understand Protein Structure, Dynamics and Function" https://doi.org/10.3389/fmolb.2022.906437.

  • Using spectroscopic changes as a ruler for protein activation: Bostock & Nietlispach et al. (2020) Curr Opin Struct Biol "The role of NMR spectroscopy in mapping the conformational landscape of GPCRs" https://doi.org/10.1016/j.sbi.2019.03.030.

  • In cell studies: Siegal & Selenko (2019) J Magn Res "Cells, drugs and NMR" https://doi.org/10.1016/j.jmr.2019.07.018.

  • An optimisation and quality control tool on unlabelled proteins: Ban & McCoy et al. (2021) MAbs "Quantification of natural abundance NMR data differentiates the solution behavior of monoclonal antibodies and their fragments" https://doi.org/10.1080/19420862.2021.1978132 ; Ma & Miller et al. (2023) J Pharm Biomed Anal "NMR spectroscopy as a characterization tool enabling biologics formulation development"  doi: 10.1016/j.jpba.2022.115110.